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Wicked-fast transcript quantification with Salmon

Traditionally, in order to quantify transcript abundance from RNA-Seq, one has to first align the reads onto the reference and analyse these alignments. While widely accepted, this approach has several disadvantages:

On my data, Salmon is ~3 times faster (6-7min) and uses ~20 times less memory (1.1GB) than STAR (~20min / ~24GB). Note, STAR results (.bam) need to be further analysed (ie. cufflinks) in order to quantify transcripts abundances. This step takes another 10min, thus we get transcript abundances after 6-7 min from Salmon and 30min from STAR + cufflinks. Just for comparison, similar analysis done with tophat2 takes above 6 hours!